To isolate lyme disease bacteria, yale researchers “go fishing”

Yale researchers became the first group to sequence the full genome of the bacteria that causes Lyme disease.

Using a novel genetic approach, the team isolated and analyzed the genome of Borrelia burgdorferi, the bacteria that causes Lyme disease in humans. The paper explaining their methodology was published in Nature Ecology & Evolution on Aug. 28.

“We found that one disease’s evolutionary history is much more complex than we thought — the diversity is much more ancient — and that the recent Lyme disease epidemic does not mirror evolutionary changes but rather anthropological and ecological changes that have an impact on the tick population,” said Giovanna Carpi, a former Yale postdoctoral researcher and a co-author of the paper.

According to the study, first author Katharine Walter GRD ’17 and her colleagues collected and sequenced 146 Borrelia genomes, with samples ranging in age from five to 33 years old.

School of Public Health professor and co-author Gisella Caccone GRD ’86 said a study like theirs could have been done one of two ways: by culturing a pure sample of the target bacterial DNA in the lab or by collecting and isolating samples from ticks. Since the researchers wanted to look at how the bacterial genome in Borrelia might have evolved and migrated in the U.S. as well as account for genetic variation within the species, they chose the second option.

Walter said she and her sister collected the samples for the study in summer 2013.

“We basically just camped out and collected ticks all summer long, and over the course of about a month and a half during the summer, we collected more than 7,000 ticks, so ticks were not in short supply in New England,” she said.

She added that other collaborators in the Midwest and Canada also sent samples for the study.

Next, researchers screened the ticks for Lyme disease, applying their novel sequencing technique on those that tested positive for the pathogen.

The study hinged on the team’s application of a technique Caccone described as “fishing a needle from a haystack with a magnet.” She explained that the method relies on genetic “hooks” that are sequence-specific to the genome of the tick and not the bacteria. By adding these “hooks” to a solution of mixed tick and bacterial DNA, the tick DNA will hybridize, rendering it stuck in the solution while the bacterial DNA can be removed and sequenced normally.

Carpi, who designed the methodology used to isolate the Borrelia genome, said the team had previously published a paper describing the technique but that this was the first large-scale study of its application to Lyme disease bacteria.

The study cited the current state of genetic sequencing as a potential limitation to the findings, since researchers were only able to reconstruct one bacterial genome from an infected tick even though there may have been multiple strains implicated in the infection. Walter added that older samples would have helped in understanding the rate at which the bacteria evolves, since the oldest samples used by the team were from the 1980s.

“When you’re doing evolutionary history, it’s an incomplete story, and it’s a story told by the samples you have,” Walter said.

Now that the researchers have developed an effective technique to isolate bacterial DNA from that of their host, they can apply it to other vector-borne diseases, such as malaria and African sleeping sickness, Caccone said.

She added that while the study did not advance treatment, it may help predict future movement of the disease. Notably, the researchers found that some strains of the bacteria were conserved even across thousands of miles, suggesting Borrelia can undergo long-range migration via birds.

Walter said this particular finding is significant in understanding both that Lyme disease is an ongoing epidemic and that its spread over the last 40 years has been triggered by human activity.

“This is definitely not the only infectious disease that is re-emerging now because of human-imposed environmental and ecological change,” she said. “I think it’s important to keep investigating and asking questions about how human health is influenced by changing ecology.”

Lyme disease was first described as a tick-borne illness in 1976 in Lyme, Connecticut.